Neurodegenerative diseases such as Huntington disease, Parkinson's disease, and Alzheimer's disease are caused by the accumulation of aggregate prone proteins. Pathogenic proteins misfold, aggregate, and escape the cell's normal degradative pathways. Protein aggregates subsequently lead to the toxic disruption of normal cellular processes leading, ultimately, to disease. Several lines of evidence suggest that reducing the burden of these toxic aggregates is therapeutic. One mechanism proposed to facilitate the degradation or clearance of these protein inclusions is macroautophagy. While autophagic treatment paradigms for neurodegeneration are still in the early stages of preclinical development, it is essential to identify and validate methods to measure the activation of autophagy in human patients. These methods will serve as important biomarkers necessary to test compound efficacy and monitor clinical improvement.